John Portwood
2014-04-07 21:15:11 UTC
Hello,
I'm having a problem with GBrowse2 (v 2.43) and the link to the archive
mailing list wasn't working so I'm not able to see if this has been
reported before.
For only one track, when the name is searched in GBrowse the browser will
navigate to a section that is slightly off from where the name is located.
For example take this section from my GFF3 (rendered from grepping
"GRMZM2G124745"):
Chr7 AGPv3 protein_coding_gene 176806695 176810119 .
+ .
Name=GRMZM2G124745;biotype=protein_coding;logic_name=genebuilder;ID=GRMZM2G124745
Chr7 AGPv3 transcript 176806695 176810119 . +
.
Name=GRMZM2G124745_T01;Parent=GRMZM2G124745;biotype=protein_coding;description=est;logic_name=genebuilder;ID=GRMZM2G124745_T01
Chr7 AGPv3 exon 176806695 176806968 . + .
Name=GRMZM2G124745_E04;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;rank=1;ID=GRMZM2G124745_E04
Chr7 AGPv3 five_prime_UTR 176806695 176806706 . +
. Parent=GRMZM2G124745_T01;
Chr7 AGPv3 CDS 176806707 176806968 . + 0
Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=1;ID=GRMZM2G124745_P01
Chr7 AGPv3 CDS 176808089 176808340 . + 0
Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=2;ID=GRMZM2G124745_P01
Chr7 AGPv3 exon 176808089 176808340 . + .
Name=GRMZM2G124745_E03;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;rank=2;ID=GRMZM2G124745_E03
Chr7 AGPv3 CDS 176808921 176809060 . + 0
Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=3;ID=GRMZM2G124745_P01
Chr7 AGPv3 exon 176808921 176809060 . + .
Name=GRMZM2G124745_E01;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_phase=1;rank=3;ID=GRMZM2G124745_E01
Chr7 AGPv3 CDS 176810033 176810119 . + 0
Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=4;ID=GRMZM2G124745_P01
Chr7 AGPv3 exon 176810033 176810119 . + .
Name=GRMZM2G124745_E02;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_end_phase=-1;rank=4;ID=GRMZM2G124745_E02
Searching for "GRMZM2G124745" in GBrowse will bring me to this region:
*Chr7:176,822,753..176,826,177*
However, on the first line in the above snippet you can see this element is
actually located between 176,806,695 and 176,810,119 on Chr7. All of the
elements are being rendered at their correct positions specified in the gff
-- It's only when you search for them by name the browser takes you to a
region ahead of them.
This problem is not occurring with other tracks that I have loaded, so I'm
guessing there's a problem either with the gff or the config file but after
much research I'm still unable to find the cause of this issue.
Any help is greatly appreciated. Thanks!
-John
I'm having a problem with GBrowse2 (v 2.43) and the link to the archive
mailing list wasn't working so I'm not able to see if this has been
reported before.
For only one track, when the name is searched in GBrowse the browser will
navigate to a section that is slightly off from where the name is located.
For example take this section from my GFF3 (rendered from grepping
"GRMZM2G124745"):
Chr7 AGPv3 protein_coding_gene 176806695 176810119 .
+ .
Name=GRMZM2G124745;biotype=protein_coding;logic_name=genebuilder;ID=GRMZM2G124745
Chr7 AGPv3 transcript 176806695 176810119 . +
.
Name=GRMZM2G124745_T01;Parent=GRMZM2G124745;biotype=protein_coding;description=est;logic_name=genebuilder;ID=GRMZM2G124745_T01
Chr7 AGPv3 exon 176806695 176806968 . + .
Name=GRMZM2G124745_E04;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;rank=1;ID=GRMZM2G124745_E04
Chr7 AGPv3 five_prime_UTR 176806695 176806706 . +
. Parent=GRMZM2G124745_T01;
Chr7 AGPv3 CDS 176806707 176806968 . + 0
Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=1;ID=GRMZM2G124745_P01
Chr7 AGPv3 CDS 176808089 176808340 . + 0
Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=2;ID=GRMZM2G124745_P01
Chr7 AGPv3 exon 176808089 176808340 . + .
Name=GRMZM2G124745_E03;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;rank=2;ID=GRMZM2G124745_E03
Chr7 AGPv3 CDS 176808921 176809060 . + 0
Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=3;ID=GRMZM2G124745_P01
Chr7 AGPv3 exon 176808921 176809060 . + .
Name=GRMZM2G124745_E01;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_phase=1;rank=3;ID=GRMZM2G124745_E01
Chr7 AGPv3 CDS 176810033 176810119 . + 0
Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=4;ID=GRMZM2G124745_P01
Chr7 AGPv3 exon 176810033 176810119 . + .
Name=GRMZM2G124745_E02;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_end_phase=-1;rank=4;ID=GRMZM2G124745_E02
Searching for "GRMZM2G124745" in GBrowse will bring me to this region:
*Chr7:176,822,753..176,826,177*
However, on the first line in the above snippet you can see this element is
actually located between 176,806,695 and 176,810,119 on Chr7. All of the
elements are being rendered at their correct positions specified in the gff
-- It's only when you search for them by name the browser takes you to a
region ahead of them.
This problem is not occurring with other tracks that I have loaded, so I'm
guessing there's a problem either with the gff or the config file but after
much research I'm still unable to find the cause of this issue.
Any help is greatly appreciated. Thanks!
-John